


The Merlin Files

by DabblesinDrabbles



Category: Merlin (TV)
Genre: M/M, The X-Files References
Language: English
Status: In-Progress
Published: 2015-08-11
Updated: 2015-08-22
Packaged: 2018-04-14 04:59:46
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 2
Words: 2,752
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/4551444
Author URL: https://archiveofourown.org/users/DabblesinDrabbles/pseuds/DabblesinDrabbles
Summary: <blockquote class="userstuff">
              <p>Agents Merlin Emrys and Arthur Pendragon work in the mysterious (some say cursed) X-Files division but there's more to these cases then meets the eye. Between government and magical conspiracies, their friends and coworkers insisting there is more than just friendship between them, and Merlin's magical secret it's going to be an interesting ride.</p>
            </blockquote>





	1. The FBI's Most Unwanted

**Author's Note:**

> As this is the first chapter it's kinda slow but I hope the idea will be enough to keep you reading as the chapters continue! This is my first, published, story so I hope you enjoy if you have any criticisms or advice feel free to leave comments! I'll be trying to update every week and also sorry for what I know will be very cheesy references to X-Files but it's one of my favorite shows 
> 
>  
> 
> Disclaimer: I am in no way associated with BBC Merlin or it's characters nor am I associated with The X-Files. :)

     To say Merlin Emrys was having a bad morning would be a grave understatement, if you had asked him he would have called it a disaster and it was still only ten in the morning. He had awoken to the screech of his analog alarm clock, the one his best friend Gwen insisted was archaic and hipster, as he rolled over to smash the snooze button he overestimated and knocked the offending clock off of his bedside table and under his bed it’s shrilling sound still piercing through the air. He pulled himself blearily through his morning routine; putting on his coffee machine (if he had used his magic this morning to do it that was no one’s business) before jumping in the shower. After trying and failing to make his hair look somewhat less messy and dressing in his G-Man suit as his partner Arthur always liked to call it he felt a little more ready to take on the day.

     This feeling of preparedness faded quickly, he realized he had forgotten his FBI badge on his bedside table, having to double back and retrieve it also made him miss his usual train, by 9:00 his partner Arthur was calling nonstop berating him for being late once again. All of this lead to Merlin barging an hour late for work into the basement office they shared, the office they both endearingly referred to as the FBI’s Most Unwanted, and sat down in a huff. Arthur who had been reclining in his desk chair throwing pencils until they stuck to the ceiling was used to Merlin’s grumpiness simply laughed and allowed his partner to have a few quiet moments before briefing him on the meeting they were to have with Assistant Director Gaius.

   Those who knew Agents Emrys and Pendragon at the beginning of their partnership, or they themselves for that matter, would have never predicated that the two men would make not only such a good investigative team but amazing friends as well. In fact if you had asked Merlin the first week of Arthur being assigned as his new partner a year ago he would have told you that Arthur Pendragon was the most narrow minded, unimaginative prat to ever grace the FBI now though while he would still call Arthur a prat but it was with a tone of fondness and a smile that would make his entire face light up. Arthur Pendragon had joined the FBI in the beginning as a very forceful middle finger to his father Senator Uther Pendragon, who had expected his only son to carry on the family political dynasty, but quickly fell in love with the gallantry that came with capturing criminals and protecting the people of Albion, he never expected however to be dumped into the basement office to virtually babysit the “crackpot” Agent Merlin Emrys and his weird pet project/division aptly named The X-Files.

   Their first assignment had hit too close to home for Arthur, a mother of three had suddenly fallen ill set under a curse by a suspected sorceress, his own mother had been taken from him before had been able to speak by a mysterious magical illness. His surliness matched with Merlin’s indignation at being babysat by another agent had lead to multiple arguments and yet by the end of the case they had not only located the sorceress and made her lift the curse but also had her registered with the government and behind bars for six months of unapproved and dangerous magic usage. Merlin and Arthur begrudgingly admitted that they made a competent team despite their opposing views on magic and those who used it, Merlin insisting that magic in itself was not evil while Arthur viewed magic as something that corrupted any who had it. It was this disagreement that made Merlin realize no matter how close he had become with his partner he would never be able to fully trust him with the burden of his secret.

    Merlin Emrys had been born to a kind mother, Hunith who never had a hint of magic except in her extraordinary capacity to love and teach her students. She was as normal as they came and until he was two years old had suspected, maybe even hoped, that Merlin had taken after her. This hope was dashed however when after throwing a tantrum, as two year old boys were aught to do, Merlin had risen in the air propelled by his own anger and his shrieking had broken every mirror in the house. Hunith knew her little boy was special, his power only growing as he got older, but she also knew how Albion’s government viewed magic and those who possessed it as second class citizens, they were not allowed the same opportunities so instead knowing what she was risking she made sure Merlin understood that his magic must be a secret, a secret he still held close to his chest even now at 25 years old.

    Merlin could never be sure what made him choose to work for the FBI, a job where if he accidently exposed his magic he wouldn’t be able to escape whatever harsh consequences would come, or even what had made him latch onto the previously abandoned X-Files division yet here he was investigating crimes which fell under the suspicion of magic or the paranormal. He had been fine working the cases alone, he enjoyed the peace of his own office, and the way the others would jokingly call him Warlock under their breaths as if it were an insult not knowing that they were closer to the truth then they had realized. His solitary existence had been shattered by the arrival of the newly minted FBI golden boy Arthur Pendragon. Merlin had expected Arthur to run, to try and debunk all of his work within the first week but instead had found within his new partner a best friend, though skeptic of magic through and through, a confidante, and someone whose loyalty Merlin valued over everyone else’s. His thoughts were interrupted by Arthur nudging his shoulder, “Come on you lazy git, we have to be up in Gaius’ office in five.” Merlin dragged himself from behind his desk, running a hand through his hair and followed Arthur to the elevator already dreading what he knew would be a dull meeting.


	2. The Cigarette Smoking Woman

**Summary for the Chapter:**

> A new case, AD Gaius, Ice Queen, and The Cigarette Smoking Woman

**Notes for the Chapter:**

> I just started back to college classes so I'm very sorry this chapter is late being updated! I'm going to try and update on time from now on. This chapter picks up a little more with mysterious new characters, friendly old ones, and a brand new case. I'm from Georgia so I decided to send Merlin and Arthur there. Please leave comments and advice if you feel like doing so, any advice is greatly appreciated!
> 
> As usual I am in no way affiliated with BBC Merlin or X-Files and make no profit from this work.

          Assistant Director Gaius was not a mean man, sure he was intimidating in the way any FBI agent had to be but for the most part Merlin and Arthur considered themselves lucky that AD Gaius was in charge of their division. As they stumbled into his office over ten minutes late for their meeting however they were met by what Merlin had affectionately, and maybe drunkenly, dubbed the “one eyebrow raise of doom.” Arthur opened his mouth to give Gaius the reason they were so late but quickly snapped it shut when he turned to see a woman standing in the shadowy corner of the office, “Sorry Director Gaius we weren’t aware you had…company.” Gaius nodded tossing an unconcerned look to where the mysterious woman was still standing, a freshly lit cigarette dangling from her fingers, “Yes, well I’ve learned to expect you and Emrys to never be on time, the reasons don’t matter. Please sit down so I can brief you two on your next case.”

       Merlin did not trust easily, understandably due to the secret he had to keep, but the woman in the corner of Gaius’ office made him feel even more uneasy than most. She had dark blue eyes that seemed to lay bare all of his secrets, her hair pulled into a slick, business like bun was a dark brown, and her lips wrapped around the end of her cigarette were a blood red color. Merlin’s magic surged, startling him as he looked at the woman, it seemed for a second she too had sensed his magic as her eyes widened and she began to smirk. Merlin turned quickly away from her knowing look, trying to focus on the conversation between Arthur and Gaius while pretending that the strange moment had not just passed. “There has been a series of kidnapping in a small town in Georgia,” Gaius began, picking up a folder from his desk and handing it to Merlin, “many in the town are suspecting Druid sacrifices.” Arthur shifted uneasily as he felt Merlin tense beside him, sensing the rant building before it bubbled over, “That is ridiculous,” Merlin hissed out as his hands clenched, “the Druids are peaceful! They do not sacrifice anyone, especially not children!” Gaius rubbed his temples, allowing Merlin a few seconds to calm down before he spoke in his usual fatherly tone, “Yes, Emrys we know that but for now we have a town and it’s people plagued by fear and hysteria, the quicker you two can track down the actual kidnappers the quicker we can proof the innocence of the Druids.”

      Gaius had been working with the FBI for many years before Merlin Emrys had come knocking on his office door, but he had never met an agent so determined and passionate until the young man had marched into his office with a request, or demand, to be allowed access to the X-Files project. The young man’s enthusiasm was infectious, something Gaius himself had once felt as a fresh from Quantico agent once upon a time, and it was this same enthusiasm that made Gaius feel as if he had to support Emrys in his quest to prove that magic could be used as a force for good. It had been an accident discovering Merlin’s magic, he had been in his office preparing his notes for a meeting, only slightly listening as the young Emrys was ranting about a case when his elbow knocked over his scalding hot coffee he had braced himself to feel the hot liquid hit his legs but the pain never came. He saw his cup suspended in midair with a wide, golden-eyed Merlin holding his hand over it. This was the day Gaius should have turned Merlin in for being an undocumented magic user but instead he made another more radical decision, he kept the agent’s secret, he didn’t know what it was that had compelled him to keep Merlin’s secret but he knew somewhere deep in his old bones that it was his duty somehow to guide Emrys into whatever was in store for him.

      This fatherly protection was given to Arthur Pendragon as well when he became Merlin’s partner, though Gaius had agreed that Merlin’s magic should be kept secret from him, Gaius could never say it but the two boys were his favorite agents. When Gaius had gotten the call that a woman named Nimueh would be evaluating his interactions with the agents in his division he had no doubt it was somehow connected to Senator Uther Pendragon’s campaign to tighten the reigns on the FBI and any organization which investigated magic. Nimueh had slunk into his office like a snake in six inch heels, ignoring his request that she not smoke, and stood in her shadowy corner eyes sharp and lips in a smirk that gave her a shark-like look, a shark that sensed blood in the water when she looked at Merlin’s outburst. Gaius seeing the look in her eyes decided they needed to be away from her immediately, “You boys will be heading down to Georgia in the morning but first take the mission briefs to Morgana and Gwen so you can get your transportation and fire arms sorted out.” He watched as Arthur and Merlin shuffled out of his office, Merlin hesitating to look back at Nimueh one more time before closing the door behind them.

       “Who even was that creepy lady,” Arthur asked as they waited for the elevator, “why was she smoking in the building? It's a bit dramatic if you ask me.” Merlin only shook his head and made a noncommittal noise, still not being able to shake the eerie feeling the woman had given him. Arthur noticed Merlin’s distraction and smirked, “She certainly seemed interested in you though,” he tugged on one of Merlin’s ears, “she kept her eyes on you like you were a meal or something.” The tug on his ear brought Merlin fully back into the conversation just as the elevator doors slid open and they stepped inside, “Yeah right,” he snorted incredulously looking at Arthur fully now, “as if anyone ever looks at me when I’m beside you the Great Golden Prat.” He pulled on a piece of Arthur’s golden hair laughing when Arthur pouted, “I am not a prat Emrys! I thought we were past this part of our partnership!” The elevator stopped and opened before Merlin could answer, instead he punched Arthur in the shoulder with a smile before stepping out on to the floor that was known by everyone as Morgana’s Lair.

      Morgana Pendragon was a 5”5 force to be reckoned with, her nickname throughout the FBI was Ice Queen and she reveled in the power of it. She had joined the FBI straight out of high school after being recruited thanks to her brilliance in perfecting and creating technology, the added bonus being that she also pissed off her stepfather Uther by deciding to not become a trophy wife for any of the sons of his Senator friends. She worked her ass off, moving through the academy with ease and graduating early along with her friend and partner in crime Gwen. Where Morgana was the Ice Queen Gwen was the gust of warmth that would make her brilliant best friend more welcoming, they worked well together a mirror to Merlin and Arthur in ways they all never chose to acknowledge. “Well hello little brother,” Morgana raised her eyes from the paperwork that cluttered her desk, “got a new assignment already?” Arthur glared at being called her little brother but knew to argue against it would cause unnecessary strife instead he grit his teeth in a smile, “Yeah we just got told by AD Gaius that we’ll be going to Georgia to investigate some Druid kidnappings.” “The Druids aren’t kidnapping anyone,” Merlin snapped, Morgana’s eyes softened as she looked at him, “Merlin, if they are innocent you’ll be the one to bring it to light.” Arthur looked back and forth between his partner and step-sister, uncomfortable with the fondness that had made it’s way into Morgana’s voice. “Morgana,” his voice came out sharper than intended, “look we just need some tech and we need Gwen to book our flight and do all the hotel stuff.” Morgana rolled her eyes fondly at Arthur’s spark jealousy and stood up from her desk stretching exaggeratedly, “Fine Prince Charming let me go find Gwen, I think she’s still in the lab.”

    Where Morgana had greeted the pair with sarcasm Gwen greeted them with a smile and her customary offer of coffee, the former of which was returned and the latter declined. She quickly got to work calling airlines, a car service, and hotels near the town they would be investigating while Morgana went into the gun inventory and picked out the guns that would be best suited for them. After they had everything settled and knew their flight schedule Arthur and Merlin thanked the girls and headed back to their office, the discomfort from seeing the mystery woman in Gaius’ office returned to Merlin as he stood with Arthur in the elevator. He thought back to the surge in his magic, the uncontrolled reaction something he hadn’t dealt with since he was a teenager and grimaced. Arthur saw his frown and awkwardly patted his shoulder, “Listen Merlin if you and Morgana are well you know,” he ran a hand through his hair awkwardly trying to avoid Merlin’s curious eyes that were now looking at him, “look what I’m saying is if you want to date Morgana I won’t be weird about it.” Merlin blurted a laugh before he could help himself, doubling over with the force of his own laughter before looking at the seriousness of Arthur’s expression, he straightened up and tried to normalize his tone as the elevator opened into the basement, “Arthur, I am in no way interested in Morgana,” he stepped out quickly, “I prefer blondes.” He turned towards the office door, the tips of his ears reddening, completely missing the small, satisfied smile that crept it’s way across Arthur’s lips.


End file.
